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Please direct usage questions or support issues to the mailing list:

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rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

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AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

CONTRIBUTORS

Gary Williams G.Williams@hgmp.mrc.ac.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title : new
Usage : my $obj = Bio::SearchIO::Writer::HTMLResultWriter->new();
Function: Builds a new Bio::SearchIO::Writer::HTMLResultWriter object
Returns : Bio::SearchIO::Writer::HTMLResultWriter
Args : -filters => hashref with any or all of the keys (HSP HIT RESULT)
which have values pointing to a subroutine reference
which will expect to get a
-nucleotide_url => URL sprintf string base for the nt sequences
-protein_url => URL sprintf string base for the aa sequences
-no_wublastlinks => boolean. Do not display WU-BLAST lines
even if they are parsed out.
Links = (1)

remote_database_url

Title : remote_database_url
Usage : $obj->remote_database_url($type,$newval)
Function: This should return or set a string that contains a %s which can be
filled in with sprintf.
Returns : value of remote_database_url
Args : $type - 'PROTEIN' or 'P' for protein URLS
'NUCLEOTIDE' or 'N' for nucleotide URLS
$value - new value to set [optional]

to_string

Purpose : Produces data for each Search::Result::ResultI in a string.
: This is an abstract method. For some useful implementations,
: see ResultTableWriter.pm, HitTableWriter.pm,
: and HSPTableWriter.pm.
Usage : print $writer->to_string( $result_obj, @args );
Argument : $result_obj = A Bio::Search::Result::ResultI object
: @args = any additional arguments used by your implementation.
Returns : String containing data for each search Result or any of its
: sub-objects (Hits and HSPs).
Throws : n/a

hit_link_desc

Title : hit_link_desc
Usage : $self->hit_link_desc(\&link_function);
Function: Get/Set the function which provides an HTML
link(s) for the given hit to be used
within the description section at the top of the BLAST report.
This allows a person reading the report within
a web browser to go to one or more database entries for
the given hit from the description section.
Returns : Function reference
Args : Function reference
See Also: L<default_hit_link_desc()>

default_hit_link_desc

Title : default_hit_link_desc
Usage : $self->default_hit_link_desc($hit, $result)
Function: Provides an HTML link(s) for the given hit to be used
within the description section at the top of the BLAST report.
This allows a person reading the report within
a web browser to go to one or more database entries for
the given hit from the description section.
Returns : string containing HTML markup "<a href...")
The default implementation returns an HTML link to the
URL supplied by the remote_database_url() method
and using the identifier supplied by the id_parser() method.
It will use the NCBI GI if present, and the accession if not.
Args : First argument is a Bio::Search::Hit::HitI
Second argument is a Bio::Search::Result::ResultI

hit_link_align

Title : hit_link_align
Usage : $self->hit_link_align(\&link_function);
Function: Get/Set the function which provides an HTML link(s)
for the given hit to be used
within the HSP alignment section of the BLAST report.
This allows a person reading the report within
a web browser to go to one or more database entries for
the given hit from the alignment section.
Returns : string containing HTML markup "<a href...")
The default implementation delegates to hit_link_desc().
Args : First argument is a Bio::Search::Hit::HitI
Second argument is a Bio::Search::Result::ResultI

hit_desc_line

Title : hit_desc_line
Usage : $self->hit_desc_line(\&link_function);
Function: Get/Set the function which provides HTML for the description
information from a hit. This allows one to parse
the rest of the description and split up lines, add links, etc.
Returns : Function reference
Args : Function reference
See Also: L<default_hit_link_desc()>

default_hit_desc_line

Title : default_hit_desc_line
Usage : $self->default_hit_desc_line($hit, $result)
Function: Parses the description line information, splits based on the
hidden \x01 between independent descriptions, checks the lines for
possible web links, and adds HTML link(s) for the given hit to be
used.
Returns : string containing HTML markup "<a href...")
The default implementation returns an HTML link to the
URL supplied by the remote_database_url() method
and using the identifier supplied by the id_parser() method.
It will use the NCBI GI if present, and the accession if not.
Args : First argument is a Bio::Search::Hit::HitI
Second argument is a Bio::Search::Result::ResultI

start_report

Title : start_report
Usage : $index->start_report( CODE )
Function: Stores or returns the code to
write the start of the <HTML> block, the <TITLE> block
and the start of the <BODY> block of HTML. Useful
for (for instance) specifying alternative
HTML if you are embedding the output in
an HTML page which you have already started.
(For example a routine returning a null string).
Returns \&default_start_report (see below) if not
set.
Example : $index->start_report( \&my_start_report )
Returns : ref to CODE if called without arguments
Args : CODE

default_start_report

Title : default_start_report
Usage : $self->default_start_report($result)
Function: The default method to call when starting a report.
Returns : sting
Args : First argument is a Bio::Search::Result::ResultI

title

Title : title
Usage : $self->title($CODE)
Function: Stores or returns the code to provide HTML for the given
BLAST report that will appear at the top of the BLAST report
HTML output. Useful for (for instance) specifying
alternative routines to write your own titles.
Returns \&default_title (see below) if not
set.
Example : $index->title( \&my_title )
Returns : ref to CODE if called without arguments
Args : CODE

default_title

Title : default_title
Usage : $self->default_title($result)
Function: Provides HTML for the given BLAST report that will appear
at the top of the BLAST report HTML output.
Returns : string containing HTML markup
The default implementation returns <CENTER> <H1> HTML
containing text such as:
"Bioperl Reformatted HTML of BLASTP Search Report
for gi|1786183|gb|AAC73113.1|"
Args : First argument is a Bio::Search::Result::ResultI

end_report

Title : end_report
Usage : $self->end_report()
Function: The method to call when ending a report, this is
mostly for cleanup for formats which require you to
have something at the end of the document (</BODY></HTML>)
for HTML
Returns : string
Args : none

id_parser

Title : id_parser
Usage : $index->id_parser( CODE )
Function: Stores or returns the code used by record_id to
parse the ID for record from a string. Useful
for (for instance) specifying a different
parser for different flavours of FASTA file.
Returns \&default_id_parser (see below) if not
set. If you supply your own id_parser
subroutine, then it should expect a fasta
description line. An entry will be added to
the index for each string in the list returned.
Example : $index->id_parser( \&my_id_parser )
Returns : ref to CODE if called without arguments
Args : CODE

default_id_parser

Title : default_id_parser
Usage : $id = default_id_parser( $header )
Function: The default Fasta ID parser for Fasta.pm
Returns $1 from applying the regexp /^>\s*(\S+)/
to $header.
Returns : ID string
The default implementation checks for NCBI-style
identifiers in the given string ('gi|12345|AA54321').
For these IDs, it extracts the GI and accession and
returns a two-element list of strings (GI, acc).
Args : a fasta header line string